Philip Bevilacqua All publications ( 47 ) Nallagatla SR. Bevilacqua PC. Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure-specific manner. 2008 Jun. RNA. 14(6):1201-13. Cerrone-Szakal AL. Chadalavada DM. Golden BL. Bevilacqua PC. Mechanistic characterization of the HDV genomic ribozyme: The cleavage site base pair plays a structural role in facilitating catalysis. 2008 Jul 24. RNA. . Gong B. Chen JH. Chase E. Chadalavada DM. Yajima R. Golden BL. Bevilacqua PC. Carey PR. Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography. 2007 Oct 31. J Am Chem Soc. 129(43):13335-42. Bevilacqua PC. Blose JM. Structures, Kinetics, Thermodynamics, and Biological Functions of RNA Hairpins. 2007 Oct 15. Annu Rev Phys Chem. . Nallagatla SR. Hwang J. Toroney R. Zheng X. Cameron CE. Bevilacqua PC. 5'-triphosphate-dependent activation of PKR by RNAs with short stem-loops. 2007 Nov 30. Science. 318(5855):1455-8. McGraw AP. Bevilacqua PC. Babitzke P. TRAP-5' stem loop interaction increases the efficiency of transcription termination in the Bacillus subtilis trpEDCFBA operon leader region. 2007 Nov. RNA. 13(11):2020-33. Bevilacqua PC. Cerrone-Szakal AL. Siegfried NA. Insight into the functional versatility of RNA through model-making with applications to data fitting. 2007 Mar 29. Q Rev Biophys. 1-31. Nakano S. Bevilacqua PC. Mechanistic characterization of the HDV genomic ribozyme: a mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons. 2007 Mar 20. Biochemistry. 46(11):3001-12. Public Health Service Bevilacqua PC. SantaLucia J. The biophysics of RNA. 2007 Jul 20. ACS Chem Biol. 2(7):440-4. Siegfried NA. Metzger SL. Bevilacqua PC. Folding cooperativity in RNA and DNA is dependent on position in the helix. 2007 Jan 9. Biochemistry. 46(1):172-81. Yajima R. Proctor DJ. Kierzek R. Kierzek E. Bevilacqua PC. A conformationally restricted guanosine analog reveals the catalytic relevance of three structures of an RNA enzyme. 2007 Jan. Chem Biol. 14(1):23-30. Fogarty International Center Chadalavada DM. Cerrone-Szakal AL. Bevilacqua PC. Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions. 2007 Dec. RNA. 13(12):2189-201. Blose JM. Silverman SK. Bevilacqua PC. A simple molecular model for thermophilic adaptation of functional nucleic acids. 2007 Apr 10. Biochemistry. 46(14):4232-40. Bevilacqua PC. Yajima R. Nucleobase catalysis in ribozyme mechanism. 2006 Oct. Curr Opin Chem Biol. 10(5):455-64. Public Health Service Brown TS. Bevilacqua PC. Method for assigning double-stranded RNA structures. 2005 Mar. Biotechniques. 38(3):368, 370, 372. National Institute of General Medical Sciences Bevilacqua PC. Brown TS. Chadalavada D. Lecomte J. Moody E. Nakano SI. Linkage between proton binding and folding in RNA: implications for RNA catalysis. 2005 Jun. Biochem Soc Trans. 33(Pt 3):466-70. Moody EM. Lecomte JT. Bevilacqua PC. Linkage between proton binding and folding in RNA: a thermodynamic framework and its experimental application for investigating pKa shifting. 2005 Feb. RNA. 11(2):157-72. National Institute of General Medical Sciences Proctor DJ. Ma H. Kierzek E. Kierzek R. Gruebele M. Bevilacqua PC. Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate. 2004 Nov 9. Biochemistry. 43(44):14004-14. Fogarty International Center Moody EM. Feerrar JC. Bevilacqua PC. Evidence that folding of an RNA tetraloop hairpin is less cooperative than its DNA counterpart. 2004 Jun 29. Biochemistry. 43(25):7992-8. Bevilacqua PC. Brown TS. Nakano S. Yajima R. Catalytic roles for proton transfer and protonation in ribozymes. 2004 Jan. Biopolymers. 73(1):90-109. Paxon TL. Brown TS. Lin HY. Brancato SJ. Roddy ES. Bevilacqua PC. Ewing AG. Continuous monitoring of enzyme reactions on a microchip: application to catalytic RNA self-cleavage. 2004 Dec 1. Anal Chem. 76(23):6921-7. Zheng X. Bevilacqua PC. Activation of the protein kinase PKR by short double-stranded RNAs with single-stranded tails. 2004 Dec. RNA. 10(12):1934-45. National Institute of General Medical Sciences Moody EM. Brown TS. Bevilacqua PC. Simple method for determining nucleobase pK(a) values by indirect labeling and demonstration of a pK(a) of neutrality in dsDNA. 2004 Aug 25. J Am Chem Soc. 126(33):10200-1. Brown TS. Chadalavada DM. Bevilacqua PC. Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength. 2004 Aug 13. J Mol Biol. 341(3):695-712. National Institute of General Medical Sciences Moody EM. Bevilacqua PC. Structural and energetic consequences of expanding a highly cooperative stable DNA hairpin loop. 2004 Aug 11. J Am Chem Soc. 126(31):9570-7. Schaak JE. Yakhnin H. Bevilacqua PC. Babitzke P. A Mg2+-dependent RNA tertiary structure forms in the Bacillus subtilis trp operon leader transcript and appears to interfere with trpE translation control by inhibiting TRAP binding. 2003 Sep 19. J Mol Biol. 332(3):555-74. National Institute of General Medical Sciences Proctor DJ. Kierzek E. Kierzek R. Bevilacqua PC. Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine. 2003 Mar 5. J Am Chem Soc. 125(9):2390-1. Fogarty International Center Bevilacqua PC. Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme. 2003 Mar 4. Biochemistry. 42(8):2259-65. Nakano S. Cerrone AL. Bevilacqua PC. Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism. 2003 Mar 18. Biochemistry. 42(10):2982-94. National Institute of General Medical Sciences Moody EM. Bevilacqua PC. Thermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs. 2003 Feb 26. J Am Chem Soc. 125(8):2032-3. Moody EM. Bevilacqua PC. Folding of a stable DNA motif involves a highly cooperative network of interactions. 2003 Dec 31. J Am Chem Soc. 125(52):16285-93. Schaak JE. Babitzke P. Bevilacqua PC. Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus. 2003 Dec. RNA. 9(12):1502-15. National Institute of General Medical Sciences Babitzke P. Schaak J. Yakhnin AV. Bevilacqua PC. Role of RNA structure in transcription attenuation in Bacillus subtilis: the trpEDCFBA operon as a model system. 2003. Methods Enzymol. 371:392-404. Proctor DJ. Schaak JE. Bevilacqua JM. Falzone CJ. Bevilacqua PC. Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions. 2002 Oct 8. Biochemistry. 41(40):12062-75. Diegelman-Parente A. Bevilacqua PC. A mechanistic framework for co-transcriptional folding of the HDV genomic ribozyme in the presence of downstream sequence. 2002 Nov 15. J Mol Biol. 324(1):1-16. National Institute of General Medical Sciences Nakano M. Moody EM. Liang J. Bevilacqua PC. Selection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg),d(cCNNGg), and d(gCNNGc). 2002 Dec 3. Biochemistry. 41(48):14281-92. Bevilacqua PC. Battle for the bulge: directing small molecules to DNA and RNA defects. 2002 Aug. Chem Biol. 9(8):854-5. Chadalavada DM. Senchak SE. Bevilacqua PC. The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots. 2002 Apr 5. J Mol Biol. 317(4):559-75. National Institute of General Medical Sciences Nakano S. Proctor DJ. Bevilacqua PC. Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism. 2001 Oct 9. Biochemistry. 40(40):12022-38. Nakano S. Bevilacqua PC. Proton inventory of the genomic HDV ribozyme in Mg(2+)-containing solutions. 2001 Nov 14. J Am Chem Soc. 123(45):11333-4. Zheng X. Bevilacqua PC. Efficient construction of long DNA duplexes with internal non-Watson-Crick motifs and modifications. 2001 Jan 15. Nucleic Acids Res. 29(2):E6. National Institute of General Medical Sciences Nakano S. Chadalavada DM. Bevilacqua PC. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. 2000 Feb 25. Science. 287(5457):1493-7. National Institute of General Medical Sciences Zheng X. Bevilacqua PC. Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR. 2000 Dec 19. Proc Natl Acad Sci U S A. 97(26):14162-7. National Institute of General Medical Sciences Chadalavada DM. Knudsen SM. Nakano S. Bevilacqua PC. A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme. 2000 Aug 11. J Mol Biol. 301(2):349-67. National Institute of General Medical Sciences Arnold JJ. Ghosh SK. Bevilacqua PC. Cameron CE. Single-nucleotide resolution of RNA strands in the presence of their RNA complements. 1999 Sep. Biotechniques. 27(3):450-2, 454, 456. National Cancer Institute National Institute of General Medical Sciences Shu Z. Bevilacqua PC. Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library. 1999 Nov 16. Biochemistry. 38(46):15369-79. Bevilacqua JM. Bevilacqua PC. Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin. 1998 Nov 10. Biochemistry. 37(45):15877-84.